We analyze dynamical systems of general form possessing gradient (symmetric) and Hamiltonian (antisymmetric) flow parts. The relevance of such systems to self-organizing processes is discussed. Coherent structure formation and related gradient flows on matrix Grassmann type manifolds are considered. The corresponding graph model associated with the partition swap neighborhood problem is studied. The criterion for emerging gradient and Hamiltonian flows is established. As an example we consider nonlinear dynamics in a neuron network system described by a simulative vector field. A simple criterion was written in order to establish conditions for the formation of an oscillatory pattern in a model neural system under consideration.